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This analysis uses computational modeling of clonal selection to measure evolutionary dynamics in primary human cancers. The method employs high-throughput sequencing data and simultaneously measures the selective advantage and time of appearance of subclones.
ARLNC1 is a newly discovered lncRNA that is induced by androgen receptor (AR) and maintains AR signaling by stabilizing the AR transcript. Knockdown of ARLNC1 suppresses AR expression, AR signaling and prostate cancer growth in vitro and in vivo.
Transancestral GWAS meta-analysis in 160,420 individuals identifies 139 loci associated with refractive error, including myopia. Newly identified genes implicate pathways involved in eye growth and light signaling cascades.
MTF2 is shown to directly bind DNA and recruit PRC2 in mouse embryonic stem cells. MTF2 selectively binds regions with a high density of unmethylated CpGs in a context of reduced helix twist.
VAMP-seq is a scalable assay that measures the effects of missense variants on intracellular protein abundance. Applying VAMP-seq to thousands of PTEN and TPMT variants helps to classify them as pathogenic or benign.
Integration of single-cell RNA sequencing with genome-wide association data implicates specific brain cell types in schizophrenia. Gene sets previously associated with schizophrenia implicate the same cell types, which include pyramidal cells and medium spiny neurons.
Genomic analysis of Mycobacterium tuberculosis (Mtb) isolated from tuberculosis patients identifies the transmission dynamics of Mtb in Vietnam including frequent transmission of Beijing lineage and positive selection for EsxW Beijing variant.
Genome-wide cross-trait analysis shows a strong genetic correlation between asthma and allergic diseases. Shared susceptibility loci are enriched for genes involved in immune and inflammatory responses and genes expressed in epithelial tissues.
CLASSY chromatin remodeling factors (CLSY 1–4) are shown to regulate DNA methylation in Arabidopsis, both globally and in a locus-specific manner. CLSYs and RNA polymerase IV control the production of 24-nucleotide siRNAs, which guide DNA methylation.
The authors resequence a core collection of upland cotton (Gossypium hirsutum) comprising 419 accessions. They analyze genomic variation and conduct a genome-wide association study for 13 fiber quality and yield traits in 12 different environments.
This study shows that UTX (KDM6A) suppresses myeloid leukemogenesis through noncatalytic functions. UTX loss leads to alterations in H3K27ac, H3K4me1 and chromatin accessibility, and in gene-regulatory programs mediated by ETS and GATA transcription factors.
A genome-wide association meta-analysis of individuals with clinically assessed or self-reported depression identifies 44 independent risk loci. Comparisons with other psychiatric disorders and candidate gene analyses provide new insights into major depressive disorder.
The MR-PRESSO test detects and corrects horizontal pleiotropy in multi-instrument Mendelian randomization (MR) analyses. Applying the MR-PRESSO test to 4,250 MR tests of complex traits and diseases finds horizontal pleiotropy in >48% of causal relationships.
Analysis of glioblastoma samples and derived neurospheres and xenografts shows that chromosomal and extrachromosomal alterations often display divergent inheritance patterns during cell culture and xenografting.
Joint analysis of new and previously published sequencing data for primary and metastatic prostate cancers identifies new candidate driver mutations and provides insights into disease progression and potential drug targets.
Linking transcription factors with disease loci implicates EBNA2, encoded by Epstein–Barr virus, in autoimmune diseases. Applying the method more widely identifies associations for hundreds of transcription factors, illuminating disease mechanisms.
Analysis of the imprinted KLF14 locus shows that the type 2 diabetes risk alleles in this region act in adipocytes to reduce KLF14 expression and modulate the expression of almost 400 genes in trans, leading to a shift in body-fat distribution and insulin resistance specifically in females.
Trans-ethnic analyses of exome array data identify new risk loci for type 2 diabetes. Fine-mapping analyses using genome-wide association data show that the index coding variants represent the likely causal variants at only a subset of these loci.
A transcriptome-wide association study integrating genome-wide association data with expression data from brain, blood and adipose tissues identifies new candidate susceptibility genes for schizophrenia, providing a step toward understanding the underlying biology.
Analysis of whole-genome sequences and transcription data from tumors identifies noncoding loci in which mutations affect target gene expression. These somatic eQTLs can classify tumors into pathway-based subtypes and are disrupted in 88% of tumors.